SenseLab

Computational model (s) having Python as Simulator software


 
Name
1 3D olfactory bulb: operators (Migliore et al, 2015)
2 3D-printer visualization of NEURON models (McDougal and Shepherd, 2015)
3 A contracting model of the basal ganglia (Girard et al. 2008)
4 A detailed Purkinje cell model (Masoli et al 2015)
5 A general model of hippocampal and dorsal striatal learning and decision making (Geerts et al 2020)
6 A model of ASIC1a and synaptic cleft pH modulating wind-up in wide dynamic range neurons (Delrocq)
7 A model of optimal learning with redundant synaptic connections (Hiratani & Fukai 2018)
8 A network of AOB mitral cells that produces infra-slow bursting (Zylbertal et al. 2017)
9 A simple model of neuromodulatory state-dependent synaptic plasticity (Pedrosa and Clopath, 2016)
10 A single-cell spiking model for the origin of grid-cell patterns (D'Albis & Kempter 2017)
11 A spatial model of the intermediate superior colliculus (Moren et. al. 2013)
12 A synapse model for developing somatosensory cortex (Manninen et al 2020)
13 Accurate and fast simulation of channel noise in conductance-based model neurons (Linaro et al 2011)
14 Acetylcholine Boosts Dendritic NMDA Spikes in a CA3 Pyramidal Neuron Model (Humphries et al., 2021)
15 Action potential-evoked Na+ influx similar in axon and soma (Fleidervish et al. 2010) (Python)
16 Activity patterns in a subthalamopallidal network of the basal ganglia model (Terman et al 2002)
17 Adaptive dual control of deep brain stimulation in Parkinsons disease simulations (Grado et al 2018)
18 Allen Institute: Gad2-IRES-Cre VISp layer 5 472447460
19 Allen Institute: Gad2-IRES-Cre VISp layer 5 473561729
20 Allen Institute: Htr3a-Cre VISp layer 2/3 472352327
21 Allen Institute: Htr3a-Cre VISp layer 2/3 472421285
22 Allen Institute: Nr5a1-Cre VISp layer 2/3 473862496
23 Allen Institute: Nr5a1-Cre VISp layer 4 329322394
24 Allen Institute: Nr5a1-Cre VISp layer 4 472306544
25 Allen Institute: Nr5a1-Cre VISp layer 4 472442377
26 Allen Institute: Nr5a1-Cre VISp layer 4 472451419
27 Allen Institute: Nr5a1-Cre VISp layer 4 472915634
28 Allen Institute: Nr5a1-Cre VISp layer 4 473834758
29 Allen Institute: Nr5a1-Cre VISp layer 4 473863035
30 Allen Institute: Nr5a1-Cre VISp layer 4 473871429
31 Allen Institute: Ntsr1-Cre VISp layer 4 472430904
32 Allen Institute: Pvalb-IRES-Cre VISp layer 2/3 472306616
33 Allen Institute: Pvalb-IRES-Cre VISp layer 5 471085845
34 Allen Institute: Pvalb-IRES-Cre VISp layer 5 472349114
35 Allen Institute: Pvalb-IRES-Cre VISp layer 5 472912177
36 Allen Institute: Pvalb-IRES-Cre VISp layer 5 473465774
37 Allen Institute: Pvalb-IRES-Cre VISp layer 5 473862421
38 Allen Institute: Pvalb-IRES-Cre VISp layer 6a 471081668
39 Allen Institute: Pvalb-IRES-Cre VISp layer 6a 472301074
40 Allen Institute: Pvalb-IRES-Cre VISp layer 6a 473860269
41 Allen Institute: Rbp4-Cre VISp layer 5 472424854
42 Allen Institute: Rbp4-Cre VISp layer 6a 473871592
43 Allen Institute: Rorb-IRES2-Cre-D VISp layer 2/3 472299294
44 Allen Institute: Rorb-IRES2-Cre-D VISp layer 2/3 472434498
45 Allen Institute: Rorb-IRES2-Cre-D VISp layer 4 473863510
46 Allen Institute: Rorb-IRES2-Cre-D VISp layer 5 471087975
47 Allen Institute: Rorb-IRES2-Cre-D VISp layer 5 473561660
48 Allen Institute: Scnn1a-Tg2-Cre VISp layer 4 472300877
49 Allen Institute: Scnn1a-Tg2-Cre VISp layer 4 472427533
50 Allen Institute: Scnn1a-Tg2-Cre VISp layer 4 472912107
51 Allen Institute: Scnn1a-Tg2-Cre VISp layer 4 473465456
52 Allen Institute: Scnn1a-Tg2-Cre VISp layer 5 472306460
53 Allen Institute: Scnn1a-Tg3-Cre VISp layer 4 329321704
54 Allen Institute: Scnn1a-Tg3-Cre VISp layer 4 472363762
55 Allen Institute: Scnn1a-Tg3-Cre VISp layer 4 473862845
56 Allen Institute: Scnn1a-Tg3-Cre VISp layer 4 473872986
57 Allen Institute: Scnn1a-Tg3-Cre VISp layer 5 472455509
58 Allen Institute: Scnn1a-Tg3-Cre VISp layer 5 473863578
59 Allen Institute: Scnn1a-Tg3-Cre VISp layer 5 473871773
60 Allen Institute: Sst-IRES-Cre VISp layer 2/3 471086533
61 Allen Institute: Sst-IRES-Cre VISp layer 2/3 472304676
62 Allen Institute: Sst-IRES-Cre VISp layer 4 472304539
63 Allen Institute: Sst-IRES-Cre VISp layer 5 472299363
64 Allen Institute: Sst-IRES-Cre VISp layer 5 472450023
65 Allen Institute: Sst-IRES-Cre VISp layer 5 473835796
66 Allen Institute: Sst-IRES-Cre VISp layer 6a 472440759
67 An attractor network model of grid cells and theta-nested gamma oscillations (Pastoll et al 2013)
68 Analytical modelling of temperature effects on an AMPA-type synapse (Kufel & Wojcik 2018)
69 AOB mitral cell: persistent activity without feedback (Zylbertal et al., 2015)
70 Automated metadata suggester (McDougal et al 2018)
71 Ave. neuron model for slow-wave sleep in cortex Tatsuki 2016 Yoshida 2018 Rasmussen 2017 (all et al)
72 Biophysical model for field potentials of networks of I&F neurons (beim Graben & Serafim 2013)
73 Biophysically detailed model of somatosensory thalamocortical circuit
74 Boolean network-based analysis of the apoptosis network (Mai and Liu 2009)
75 Brain networks simulators - a comparative study (Tikidji-Hamburyan et al 2017)
76 Brette-Gerstner model (Touboul and Brette 2008)
77 CA1 PV+ fast-firing hippocampal interneuron (Ferguson et al. 2013)
78 CA1 pyr cell: Inhibitory modulation of spatial selectivity+phase precession (Grienberger et al 2017)
79 CA1 pyr cell: phenomenological NMDAR-based model of synaptic plasticity (Dainauskas et al 2023)
80 CA1 pyramidal cell receptor dependent cAMP dynamics (Chay et al. 2016)
81 CA1 pyramidal neuron (Ferguson et al. 2014)
82 CA1 pyramidal neuron network model (Ferguson et al 2015)
83 CA1 SOM+ (OLM) hippocampal interneuron (Ferguson et al. 2015)
84 Ca2+ oscillations in single astrocytes (Lavrentovich and Hemkin 2008) (python) (Manninen et al 2017)
85 CA3 Network Model of Epileptic Activity (Sanjay et. al, 2015)
86 Calculating the consequences of left-shifted Nav channel activity in sick cells (Joos et al 2018)
87 Cellular and Synaptic Mechanisms Differentiate Mitral & Superficial Tufted Cells (Jones et al 2020)
88 Central Nervous System tadpole model in Matlab and NEURON-Python (Ferrario et al, 2021)
89 Cerebellar granule cell (Masoli et al 2020)
90 CN bushy, stellate neurons (Rothman, Manis 2003) (Brian 2)
91 CN bushy, stellate neurons (Rothman, Manis 2003) (Brian)
92 Code to calc. spike-trig. ave (STA) conduct. from Vm (Pospischil et al. 2007, Rudolph et al. 2007)
93 Coincident signals in Olfactory Bulb Granule Cell spines (Aghvami et al 2019)
94 Comparison of DA-based Stochastic Algorithms (Pezo et al. 2014)
95 Composite spiking network/neural field model of Parkinsons (Kerr et al 2013)
96 Computational modeling of gephyrin-dependent inhibitory transsynaptic signaling (Lupascu et al 2020)
97 Computer models of corticospinal neurons replicate in vitro dynamics (Neymotin et al. 2017)
98 Computing with neural synchrony (Brette 2012)
99 Concentration dependent nonlinear K+ and Cl- leak current (Huang et al. 2015)
100 Conductance-based model of rodent thoracic sympathetic postganglionic neuron (McKinnon et al 2019)
101 Connection-set Algebra (CSA) for the representation of connectivity in NN models (Djurfeldt 2012)
102 Constructed Tessellated Neuronal Geometries (CTNG) (McDougal et al. 2013)
103 Cortical Basal Ganglia Network Model during Closed-loop DBS (Fleming et al 2020)
104 Cortical feedback alters visual response properties of dLGN relay cells (Martínez-Cañada et al 2018)
105 CRH modulates excitatory transmission and network physiology in hippocampus (Gunn et al. 2017)
106 Current Dipole in Laminar Neocortex (Lee et al. 2013)
107 Dendritic Impedance in Neocortical L5 PT neurons (Kelley et al. 2021)
108 Dentate Gyrus model including Granule cells with dendritic compartments (Chavlis et al 2017)
109 Depolarization Enhacement of Dendritic Spike Propagation (Bock et al 2022)
110 Diffusive homeostasis in a spiking network model (Sweeney et al. 2015)
111 Distal inhibitory control of sensory-evoked excitation (Egger, Schmitt et al. 2015)
112 Dorsal Column Fiber Stimulation model (Gilbert et al. 2022)
113 Duration-tuned neurons from the inferior colliculus of vertebrates (Aubie et al. 2012)
114 Earthworm medial giant fiber conduction velocity across electrical synapses (Heller, Crisp 2016)
115 Effect of polysynaptic facilitaiton between piriform-hippocampal network stages (Trieu et al 2015)
116 Efficient simulation of 3D reaction-diffusion in models of neurons (McDougal et al, 2022)
117 Electrostimulation to reduce synaptic scaling driven progression of Alzheimers (Rowan et al. 2014)
118 ELL Medium Ganglion Cell (Mormyrid fish) (Muller et al, accepted)
119 ELL Medium Ganglion cell (Muller et al 2019)
120 Endocannabinoid dynamics gate spike-timing dependent depression and potentiation (Cui et al 2016)
121 Excitatory synaptic interactions in pyramidal neuron dendrites (Behabadi et al. 2012)
122 Explainable AI for spatial navigation based on hippocampal circuitry (Coppolino + Migliore 2023)
123 Fast Spiking Basket cells (Tzilivaki et al 2019)
124 Feedforward network undergoing Up-state-mediated plasticity (Gonzalez-Rueda et al. 2018)
125 Firing patterns of CA3 hippocampal neurons (Soldado-Magraner et al. 2019)
126 Fully continuous Pinsky-Rinzel model for bifurcation analysis (Atherton et al. 2016)
127 Functional balanced networks with synaptic plasticity (Sadeh et al, 2015)
128 Gamma-beta alternation in the olfactory bulb (David, Fourcaud-Trocmé et al., 2015)
129 Gap junction plasticity as a mechanism to regulate network-wide oscillations (Pernelle et al 2018)
130 Glutamate mediated dendritic and somatic plateau potentials in cortical L5 pyr cells (Gao et al '20)
131 Glutamate-evoked Ca2+ oscillations in single astrocytes (De Pitta et al. 2009) (Manninen et al 2017)
132 Glutamate-evoked Ca2+ oscillations in single astrocytes (Modified from Dupont et al. 2011)
133 Goldfish Mauthner cell (Medan et al 2017)
134 Grid cell-to-place cell transformation model w AD-related synaptic loss (Ness and Schultz 2021)
135 Hierarchical network model of perceptual decision making (Wimmer et al 2015)
136 Hippocampal CA1 pyramidal cell demonstrating dynamic mode switching (Berteau & Bullock 2020)
137 Hopfield and Brody model (Hopfield, Brody 2000) (NEURON+python)
138 Human auditory periphery model: cochlea, IHC-AN, auditory brainstem responses (Verhulst et al 2018)
139 Human L2/3 pyramidal cells with low Cm values (Eyal et al. 2016)
140 Hyperexcitability from Nav1.2 channel loss in neocortical pyramidal cells (Spratt et al 2021)
141 Ih tunes oscillations in an In Silico CA3 model (Neymotin et al. 2013)
142 Impedance spectrum in cortical tissue: implications for LFP signal propagation (Miceli et al. 2017)
143 In vivo imaging of dentate gyrus mossy cells in behaving mice (Danielson et al 2017)
144 Information transmission in cerebellar granule cell models (Rossert et al. 2014)
145 Inhibition of bAPs and Ca2+ spikes in a multi-compartment pyramidal neuron model (Wilmes et al 2016)
146 Inhibitory neuron plasticity as a mechanism for ocular dominance plasticity (Bono & Clopath 2019)
147 Inhibitory plasticity balances excitation and inhibition (Vogels et al. 2011)
148 Input strength and time-varying oscillation peak frequency (Cohen MX 2014)
149 Interplay between somatic and dendritic inhibition promotes place fields (Pedrosa & Clopath 2020)
150 Kernel method to calculate LFPs from networks of point neurons (Telenczuk et al 2020)
151 Ketamine disrupts theta modulation of gamma in a computer model of hippocampus (Neymotin et al 2011)
152 Large-scale neural model of visual short-term memory (Ulloa, Horwitz 2016; Horwitz, et al. 2005,...)
153 Layer V pyramidal cell functions and schizophrenia genetics (Mäki-Marttunen et al 2019)
154 Layer V pyramidal cell model with reduced morphology (Mäki-Marttunen et al 2018)
155 LCN-HippoModel: model of CA1 PCs deep-superficial theta firing dynamics (Navas-Olive et al 2020)
156 Leaky Integrate and Fire Neuron Model of Context Integration (Calvin, Redish 2021)
157 LFP in striatum (Tanaka & Nakamura 2019)
158 Library of biophysically detailed striatal projection neurons (Lindroos and Hellgren Kotaleski 2020)
159 Locus Coeruleus blocking model (Chowdhury et al.)
160 Maximal firing rate in midbrain dopamine neurons (Knowlton et al., 2021)
161 Mean field model for Hodgkin Huxley networks of neurons (Carlu et al 2020)
162 Mean-Field models of conductance-based NNs of spiking neurons with adaptation (di Volo et al 2019)
163 MEC layer II stellate cell: Synaptic mechanisms of grid cells (Schmidt-Hieber & Hausser 2013)
164 Mechanisms underlying subunit independence in pyramidal neuron dendrites (Behabadi and Mel 2014)
165 Memory savings through unified pre- and postsynaptic STDP (Costa et al 2015)
166 Mesoscopic dynamics from AdEx recurrent networks (Zerlaut et al JCNS 2018)
167 Mesoscopic dynamics from AdEx recurrent networks (Zerlaut et al JCNS 2018) (PyNN)
168 Minimal model of interictal and ictal discharges “Epileptor-2” (Chizhov et al 2018)
169 Model of eupnea and sigh generation in respiratory network (Toporikova et al 2015)
170 Model of peripheral nerve with ephaptic coupling (Capllonch-Juan & Sepulveda 2020)
171 Model of peristalsis in the dorsal blood vessel of Lumbriculus variegatus (Halfmann and Crisp 2011)
172 Model of Type 3 firing in neurons (Clay et al 2008)
173 Modeling a Nociceptive Neuro-Immune Synapse Activated by ATP and 5-HT in Meninges (Suleimanova et al., 2020)
174 Modeling and MEG evidence of early consonance processing in auditory cortex (Tabas et al 2019)
175 Modeling dendritic spikes and plasticity (Bono and Clopath 2017)
176 Modelling platform of the cochlear nucleus and other auditory circuits (Manis & Compagnola 2018)
177 Modelling the effects of short and random proto-neural elongations (de Wiljes et al 2017)
178 Models of visual topographic map alignment in the Superior Colliculus (Tikidji-Hamburyan et al 2016)
179 ModelView: online structural analysis of computational models (McDougal et al. 2015)
180 Modular grid cell responses as a basis for hippocampal remapping (Monaco and Abbott 2011)
181 Motion Clouds: Synthesis of random textures for motion perception (Leon et al. 2012)
182 Motor system model with reinforcement learning drives virtual arm (Dura-Bernal et al 2017)
183 Multi-timescale adaptive threshold model (Kobayashi et al 2009) (NEURON)
184 Multifunctional control of feeding in Aplysia (Webster-Wood et al. 2020)
185 MultiScale Optimized Neuronal Intramembrane Cavitation (SONIC) model (Lemaire et al. 2019)
186 Multiscale simulation of the striatal medium spiny neuron (Mattioni & Le Novere 2013)
187 Multitarget pharmacology for Dystonia in M1 (Neymotin et al 2016)
188 Muscle spindle feedback circuit (Moraud et al, 2016)
189 Na+ Signals in olfactory bulb neurons (granule cell model) (Ona-Jodar et al. 2017)
190 Network bursts in cultured NN result from different adaptive mechanisms (Masquelier & Deco 2013)
191 Network dynamics of electrically coupled pituitary cells (Fazli and Bertram, 2022)
192 Networks of spiking neurons: a review of tools and strategies (Brette et al. 2007)
193 Neural Field Simulator (Nichols & Hutt 2012-2015)
194 Neural mass model based on single cell dynamics to model pathophysiology (Zandt et al 2014)
195 NeuroGPU example on L5_TTPC1_cADpyr232_1 (Ben-Shalom 2022)(Ramaswamy et al., 2015)
196 Neuromuscular network model of gut motility (Barth et al 2017)
197 NEURON + Python (Hines et al. 2009)
198 Olfactory bulb microcircuits model with dual-layer inhibition (Gilra & Bhalla 2015)
199 Online learning model of olfactory bulb external plexiform layer network (Imam & Cleland 2020)
200 Optical stimulation of a channelrhodopsin-2 positive pyramidal neuron model (Foutz et al 2012)
201 Orientation selectivity in inhibition-dominated recurrent networks (Sadeh and Rotter, 2015)
202 Oscillations, phase-of-firing coding and STDP: an efficient learning scheme (Masquelier et al. 2009)
203 Parallel Tempering MCMC on Liu et al 1998 (Wang et al 2022)
204 Perfect Integrate and fire with noisy adaptation or fractional noise (Richard et al 2018)
205 Phase response curves firing rate dependency of rat purkinje neurons in vitro (Couto et al 2015)
206 Phase response theory in sparsely + strongly connected inhibitory NNs (Tikidji-Hamburyan et al 2019)
207 Phenomenological models of NaV1.5: Hodgkin-Huxley and kinetic formalisms (Andreozzi et al 2019)
208 PIR gamma oscillations in network of resonators (Tikidji-Hamburyan et al. 2015)
209 Place and grid cells in a loop (Rennó-Costa & Tort 2017)
210 Pleiotropic effects of SCZ-associated genes (Mäki-Marttunen et al. 2017)
211 PLS-framework (Tikidji-Hamburyan and Colonnese 2021)
212 Potjans-Diesmann cortical microcircuit model in NetPyNE (Romaro et al 2021)
213 PyMUS: A Python based Motor Unit Simulator (Kim & Kim 2018)
214 Python demo of the VmT method to extract conductances from single Vm traces (Pospischil et al. 2009)
215 Recurrent amplification of grid-cell activity (D'Albis and Kempter 2020)
216 Reduced-morphology model of CA1 pyramidal cells optimized + validated w/ HippoUnit (Tomko et al '21)
217 Resource competition in growing neurites (Hjorth et al 2014)
218 Reward modulated STDP (Legenstein et al. 2008)
219 Scaffold model of mouse CA1 hippocampus. (Gandolfi et al 2022)
220 Schiz.-linked gene effects on intrinsic single-neuron excitability (Maki-Marttunen et al. 2016)
221 SCN1A gain-of-function in early infantile encephalopathy (Berecki et al 2019)
222 SCZ-associated variant effects on L5 pyr cell NN activity and delta osc. (Maki-Marttunen et al 2018)
223 Self-organization of cortical areas in development and evolution of neocortex (Imam & Finlay 2021)
224 Sensory feedback in an oscillatory interference model of place cell activity (Monaco et al. 2011)
225 Sensory-evoked responses of L5 pyramidal tract neurons (Egger et al 2020)
226 Simulated cortical color opponent receptive fields self-organize via STDP (Eguchi et al., 2014)
227 Simulation of calcium signaling in fine astrocytic processes (Denizot et al 2019)
228 Single Trial Sequence learning: a spiking neurons model based on hippocampus (Coppolino et al 2021)
229 Somatodendritic consistency check for temporal feature segmentation (Asabuki & Fukai 2020)
230 Sound-evoked activity in peripheral axons of type I spiral ganglion neurons (Budak et al. 2021)
231 Sparse connectivity is required for decorrelation, pattern separation (Cayco-Gajic et al 2017)
232 Spatial structure from diffusive synaptic plasticity (Sweeney and Clopath, 2016)
233 Spike-Timing-Based Computation in Sound Localization (Goodman and Brette 2010)
234 Spikelet generation and AP initiation in a L5 neocortical pyr neuron (Michalikova et al. 2017) Fig 1
235 Spikelet generation and AP initiation in a simplified pyr neuron (Michalikova et al. 2017) Fig 3
236 Spiny Projection Neuron Ca2+ based plasticity is robust to in vivo spike train (Dorman&Blackwell)
237 Spontaneous calcium oscillations in single astrocytes (Riera et al. 2011) (Manninen et al 2017)
238 Spontaneous weakly correlated excitation and inhibition (Tan et al. 2013)
239 STDP allows fast rate-modulated coding with Poisson-like spike trains (Gilson et al. 2011)
240 STDP and oscillations produce phase-locking (Muller et al. 2011)
241 Stochastic versions of the Hodgkin-Huxley equations (Goldwyn, Shea-Brown 2011) (pylab)
242 Striatal D1R medium spiny neuron, including a subcellular DA cascade (Lindroos et al 2018)
243 Structure-dynamics relationships in bursting neuronal networks revealed (Mäki-Marttunen et al. 2013)
244 Switching circuit for optimal context integration during static + moving contexts (Voina et al 2022)
245 Synaptic scaling balances learning in a spiking model of neocortex (Rowan & Neymotin 2013)
246 Synchronized oscillations of clock gene expression in the choroid plexus (Myung et al 2018)
247 Tag Trigger Consolidation (Clopath and Ziegler et al. 2008)
248 The electrodiffusive Pinsky-Rinzel (edPR) model (Sætra et al., 2020)
249 Theory and simulation of integrate-and-fire neurons driven by shot noise (Droste & Lindner 2017)
250 TRPM8-dependent dynamic response in cold thermoreceptors (Olivares et al. 2015)
251 Unsupervised learning of an efficient short-term memory network (Vertechi, Brendel & Machens 2014)
252 Ventromedial Thalamocortical Neuron (Bichler et al 2021)
253 Vertical System (VS) tangential cells network model (Trousdale et al. 2014)
254 Voltage-based STDP synapse (Clopath et al. 2010)
255 Voltage-gated conductances can counteract filtering effect of membrane capacitance (Heras et al '16)